Cadmium in PDB 3rjl: Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Bacillus Licheniformis (Target Nysgrc-000337)

All present enzymatic activity of Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Bacillus Licheniformis (Target Nysgrc-000337):
1.5.1.12;

The structure of Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Bacillus Licheniformis (Target Nysgrc-000337), PDB code: 3rjl was solved by Y.Patskovsky, R.Toro, R.Foti, R.D.Seidel, S.C.Almo, New York Structuralgenomics Research Consortium (Nysgrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	103.267, 116.114, 181.768, 90.00, 90.15, 90.00
R / Rfree (%)	22.2 / 29.2

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 47;

Binding sites:

The binding sites of Cadmium atom in the Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Bacillus Licheniformis (Target Nysgrc-000337) (pdb code 3rjl). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 47 binding sites of Cadmium where determined in the Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Bacillus Licheniformis (Target Nysgrc-000337), PDB code: 3rjl:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 47 in the Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Bacillus Licheniformis (Target Nysgrc-000337)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Bacillus Licheniformis (Target Nysgrc-000337) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd539 b:43.3 occ:1.00 OE2 B:GLU343 2.2 42.0 1.0 OE2 A:GLU343 2.4 46.5 1.0 O A:HOH557 2.4 20.0 1.0 O A:HOH587 2.6 21.6 1.0 OE1 B:GLU343 2.6 27.2 1.0 OE1 A:GLU343 2.7 36.4 1.0 CD B:GLU343 2.8 39.8 1.0 CD A:GLU343 2.9 28.9 1.0 NZ A:LYS339 3.8 43.0 1.0 NE A:ARG340 4.0 51.2 1.0 CD B:ARG340 4.0 37.1 1.0 CD A:ARG340 4.1 28.0 1.0 CG B:GLU343 4.3 33.0 1.0 CE B:LYS339 4.3 34.4 1.0 CG A:GLU343 4.3 33.6 1.0 NH1 B:ARG340 4.5 43.0 1.0 CG A:LYS339 4.6 39.4 1.0 CZ A:ARG340 4.7 48.5 1.0 NE B:ARG340 4.8 35.9 1.0 CG B:LYS339 4.8 37.6 1.0 CE A:LYS339 4.9 46.8 1.0 NZ B:LYS339 4.9 26.8 1.0 CB B:GLU343 5.0 37.7 1.0

Cadmium binding site 2 out of 47 in the Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Bacillus Licheniformis (Target Nysgrc-000337)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Bacillus Licheniformis (Target Nysgrc-000337) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd540 b:88.4 occ:0.50 OD2 A:ASP393 3.0 55.3 1.0 OD1 A:ASP393 3.7 57.5 1.0 CG A:ASP393 3.8 59.6 1.0 NE2 A:GLN366 4.7 55.8 1.0

Cadmium binding site 3 out of 47 in the Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Bacillus Licheniformis (Target Nysgrc-000337)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Bacillus Licheniformis (Target Nysgrc-000337) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd541 b:86.9 occ:0.50 OE2 A:GLU352 2.1 72.2 1.0 OE1 B:GLU16 2.1 78.4 1.0 O A:HOH803 2.3 59.5 1.0 O B:HOH802 2.6 46.7 1.0 CD A:GLU352 3.2 71.8 1.0 CD B:GLU16 3.3 82.4 1.0 OE1 A:GLU352 3.7 68.9 1.0 OE2 B:GLU16 3.9 91.5 1.0 NZ A:LYS122 4.1 75.0 1.0 CG B:GLU16 4.3 72.2 1.0 CG A:GLU352 4.4 65.0 1.0 OD1 A:ASN30 5.0 83.7 1.0

Cadmium binding site 4 out of 47 in the Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Bacillus Licheniformis (Target Nysgrc-000337)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Bacillus Licheniformis (Target Nysgrc-000337) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd542 b:88.5 occ:0.50 OE1 A:GLU433 2.6 62.3 1.0 OE2 A:GLU433 2.6 59.2 1.0 CD A:GLU433 3.0 53.2 1.0 OG A:SER429 3.1 59.3 1.0 N A:SER429 4.0 53.5 1.0 O A:LYS427 4.1 45.3 1.0 CA A:VAL428 4.2 43.7 1.0 CB A:SER429 4.4 53.0 1.0 C A:VAL428 4.5 49.4 1.0 CG A:GLU433 4.5 46.8 1.0 CA A:SER429 4.9 53.0 1.0 CB A:VAL428 4.9 44.0 1.0 C A:LYS427 5.0 44.8 1.0

Cadmium binding site 5 out of 47 in the Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Bacillus Licheniformis (Target Nysgrc-000337)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Bacillus Licheniformis (Target Nysgrc-000337) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd543 b:72.3 occ:0.50 O A:HOH634 2.1 57.7 1.0 O A:HOH635 2.3 46.8 1.0 O A:HOH636 2.4 35.4 1.0 OD1 A:ASP432 3.7 66.4 1.0 CG A:ASP432 4.2 50.4 1.0 NE2 A:HIS456 4.6 28.4 1.0 N A:ASP432 4.6 37.1 1.0 OD2 A:ASP432 4.6 46.8 1.0 CB A:PHE431 4.8 39.1 1.0 CB A:ASP432 4.9 39.5 1.0 N A:PHE431 4.9 44.9 1.0

Cadmium binding site 6 out of 47 in the Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Bacillus Licheniformis (Target Nysgrc-000337)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Bacillus Licheniformis (Target Nysgrc-000337) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd544 b:76.5 occ:0.50 OD2 A:ASP455 2.7 66.6 1.0 OD1 A:ASP455 2.7 55.1 1.0 CG A:ASP455 3.0 52.9 1.0 CB A:ASP455 4.5 45.9 1.0

Cadmium binding site 7 out of 47 in the Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Bacillus Licheniformis (Target Nysgrc-000337)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Bacillus Licheniformis (Target Nysgrc-000337) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd545 b:81.0 occ:0.50 OXT A:ACT548 2.2 63.0 1.0 OE2 A:GLU224 2.8 68.4 1.0 OE1 A:GLU224 3.2 70.5 1.0 CD A:GLU224 3.4 64.6 1.0 C A:ACT548 3.4 69.1 1.0 NZ D:LYS108 3.4 56.9 1.0 O A:HOH579 3.5 43.6 1.0 O D:HOH799 3.6 38.0 1.0 CH3 A:ACT548 4.2 67.8 1.0 O A:ACT548 4.2 71.1 1.0 O D:HOH716 4.3 28.6 1.0 CE D:LYS108 4.8 52.7 1.0 NZ A:LYS108 4.8 37.9 1.0 CG2 A:VAL221 4.8 46.2 1.0 CG A:GLU224 4.9 50.3 1.0

Cadmium binding site 8 out of 47 in the Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Bacillus Licheniformis (Target Nysgrc-000337)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Bacillus Licheniformis (Target Nysgrc-000337) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd546 b:78.1 occ:0.50 OD1 A:ASP94 2.4 64.7 1.0 OD2 A:ASP94 3.0 69.9 1.0 CG A:ASP94 3.1 60.9 1.0 CG A:GLU96 3.4 57.6 1.0 CB A:GLU96 4.0 48.3 1.0 N A:GLU96 4.4 44.0 1.0 CB A:ASP94 4.6 51.3 1.0 CD A:GLU96 4.7 69.9 1.0 CA A:GLU96 4.8 46.2 1.0 OE1 A:GLU96 4.9 79.7 1.0 N A:PRO95 5.0 47.2 1.0 CD A:PRO95 5.0 44.0 1.0

Cadmium binding site 9 out of 47 in the Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Bacillus Licheniformis (Target Nysgrc-000337)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Bacillus Licheniformis (Target Nysgrc-000337) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd547 b:92.5 occ:0.50 OE1 A:GLU298 2.3 79.8 1.0 CD A:GLU298 3.1 75.8 1.0 OE2 A:GLU298 3.1 75.8 1.0 CG A:GLU298 4.5 63.0 1.0

Cadmium binding site 10 out of 47 in the Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Bacillus Licheniformis (Target Nysgrc-000337)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Bacillus Licheniformis (Target Nysgrc-000337) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd539 b:47.1 occ:0.50 O B:ACT543 2.0 56.5 1.0 O B:HOH801 2.3 63.0 1.0 OE2 B:GLU224 2.3 66.0 1.0 O B:HOH638 2.4 54.4 1.0 O B:HOH639 2.7 54.8 1.0 C B:ACT543 3.0 59.3 1.0 CD B:GLU224 3.1 63.2 1.0 OE1 B:GLU224 3.3 49.2 1.0 OXT B:ACT543 3.3 63.3 1.0 NZ B:LYS108 3.6 47.1 1.0 CH3 B:ACT543 4.3 57.4 1.0 O B:HOH800 4.4 32.9 1.0 NH1 B:ARG111 4.5 69.5 1.0 CD B:LYS108 4.5 44.6 1.0 CG B:GLU224 4.6 46.0 1.0 CG B:LYS108 4.6 39.8 1.0 CE B:LYS108 4.7 36.9 1.0 CB B:GLU224 4.9 39.5 1.0

Y.Patskovsky, R.Toro, R.Foti, R.D.Seidel, S.C.Almo. Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Bacillus Licheniformis To Be Published.